{
  "_id": "6a3b202f5cdecea1d680918f",
  "Package": "ouch",
  "Type": "Package",
  "Title": "Ornstein-Uhlenbeck Models for Phylogenetic Comparative\nHypotheses",
  "Version": "2.20-0",
  "Date": "2024-07-04",
  "Authors@R": "c(person(given=c(\"Aaron\",\"A.\"),family=\"King\",role=c(\"aut\",\"cre\"),email=\"kingaa@umich.edu\",comment=c(ORCID=\"0000-0001-6159-3207\")),\nperson(given=c(\"Marguerite\",\"A.\"),family=\"Butler\",role=c(\"ctb\")))",
  "Maintainer": "Aaron A. King <kingaa@umich.edu>",
  "Description": "Fit and compare Ornstein-Uhlenbeck models for evolution\nalong a phylogenetic tree.",
  "URL": "https://kingaa.github.io/ouch/",
  "License": "GPL-3",
  "LazyLoad": "true",
  "LazyData": "true",
  "Roxygen": "list(roclets = c(\"collate\", \"namespace\", \"rd\"), markdown =\nTRUE)",
  "RoxygenNote": "7.3.2",
  "BugReports": "https://github.com/kingaa/ouch/issues/",
  "Encoding": "UTF-8",
  "Collate": "'anolis.R' 'print.R' 'package.R' 'ouchtree.R' 'ape2ouch.R'\n'bootstrap.R' 'update.R' 'simulate.R' 'plot.R' 'summary.R'\n'logLik.R' 'coef.R' 'rmvnorm.R' 'glssoln.R' 'hansen.R'\n'brown.R' 'as_data_frame.R' 'bimac.R' 'geospiza.R' 'paint.R'",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2026-03-23 11:43:54 UTC",
  "RemoteUrl": "https://github.com/kingaa/ouch",
  "RemoteRef": "HEAD",
  "RemoteSha": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-23 23:47:42 UTC",
    "User": "root"
  },
  "Author": "Aaron A. King [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6159-3207>),\nMarguerite A. Butler [ctb]",
  "MD5sum": "186fb4de889c73b0354401cd367c5715",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "ouch_2.20-0.tar.gz",
  "_fileid": "1e3b5ef5692bf52fd623894451ea49139666c7e2fb58a9f18fe6f8e9cbbcf821",
  "_filesize": 291138,
  "_sha256": "1e3b5ef5692bf52fd623894451ea49139666c7e2fb58a9f18fe6f8e9cbbcf821",
  "_created": "2026-06-23T23:47:42.000Z",
  "_published": "2026-06-24T00:09:19.727Z",
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 83087098704,
      "time": 178,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7836488991"
    },
    {
      "job": 83087098679,
      "time": 122,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7836473016"
    },
    {
      "job": 83087098684,
      "time": 214,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836498084"
    },
    {
      "job": 83087098699,
      "time": 149,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836480924"
    },
    {
      "job": 83087098697,
      "time": 85,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7836705355"
    },
    {
      "job": 83087098706,
      "time": 215,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7836720220"
    },
    {
      "job": 83087098687,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836711561"
    },
    {
      "job": 83087098701,
      "time": 262,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836756771"
    },
    {
      "job": 83086733884,
      "time": 174,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836443704"
    },
    {
      "job": 83087098676,
      "time": 147,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836480279"
    },
    {
      "job": 83087098675,
      "time": 87,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7836465850"
    },
    {
      "job": 83087098700,
      "time": 102,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7836469307"
    },
    {
      "job": 83087098688,
      "time": 84,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7836466391"
    }
  ],
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/kingaa/ouch",
  "_commit": {
    "id": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
    "author": "Aaron A. King <kingaa@umich.edu>",
    "committer": "Aaron A. King <kingaa@umich.edu>",
    "message": "update workflows\n",
    "time": 1774266234
  },
  "_maintainer": {
    "name": "Aaron A. King",
    "email": "kingaa@umich.edu",
    "login": "kingaa",
    "orcid": "0000-0001-6159-3207",
    "description": "Nelson G. Hairston Collegiate Professor of Ecology & Evolutionary Biology, Complex Systems, and Mathematics",
    "uuid": 1863307
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "subplex",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Suggests"
    }
  ],
  "_owner": "kingaa",
  "_selfowned": false,
  "_usedby": 4,
  "_updates": [
    {
      "week": "2026-13",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "adaptive-regime",
    "brownian-motion",
    "ornstein-uhlenbeck",
    "ornstein-uhlenbeck-models",
    "ouch",
    "phylogenetic-comparative-hypotheses",
    "phylogenetic-comparative-methods",
    "phylogenetic-data",
    "react"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "kingaa",
      "count": 139,
      "uuid": 1863307
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic",
    "followers": 5
  },
  "_downloads": {
    "count": 526,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ouch"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/kingaa/ouch",
  "_searchresults": 70,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/ouch.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kingaa/ouch",
  "_realowner": "kingaa",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0-2",
      "date": "2004-10-27"
    },
    {
      "version": "1.0-3",
      "date": "2004-11-05"
    },
    {
      "version": "1.1-1",
      "date": "2005-05-25"
    },
    {
      "version": "1.1-2",
      "date": "2006-04-09"
    },
    {
      "version": "1.2-4",
      "date": "2007-06-12"
    },
    {
      "version": "2.3-11",
      "date": "2008-07-28"
    },
    {
      "version": "2.4-1",
      "date": "2008-07-29"
    },
    {
      "version": "2.4-2",
      "date": "2008-09-12"
    },
    {
      "version": "2.5-1",
      "date": "2008-12-17"
    },
    {
      "version": "2.5-2",
      "date": "2009-01-26"
    },
    {
      "version": "2.5-3",
      "date": "2009-01-30"
    },
    {
      "version": "2.5-4",
      "date": "2009-03-13"
    },
    {
      "version": "2.5-6",
      "date": "2009-07-21"
    },
    {
      "version": "2.5-7",
      "date": "2009-08-13"
    },
    {
      "version": "2.6-1",
      "date": "2010-01-21"
    },
    {
      "version": "2.6-2",
      "date": "2010-06-24"
    },
    {
      "version": "2.7-1",
      "date": "2010-07-26"
    },
    {
      "version": "2.7-2",
      "date": "2011-07-27"
    },
    {
      "version": "2.8-1",
      "date": "2011-09-01"
    },
    {
      "version": "2.8-2",
      "date": "2012-04-01"
    },
    {
      "version": "2.8-4",
      "date": "2014-03-24"
    },
    {
      "version": "2.9-2",
      "date": "2015-07-10"
    },
    {
      "version": "2.11-1",
      "date": "2017-07-18"
    },
    {
      "version": "2.14-1",
      "date": "2019-05-02"
    },
    {
      "version": "2.15-1",
      "date": "2021-02-21"
    },
    {
      "version": "2.16",
      "date": "2021-05-02"
    },
    {
      "version": "2.17",
      "date": "2021-05-17"
    },
    {
      "version": "2.18",
      "date": "2022-05-16"
    },
    {
      "version": "2.19",
      "date": "2023-04-25"
    },
    {
      "version": "2.20",
      "date": "2024-07-04"
    }
  ],
  "_exports": [
    "ape2ouch",
    "bootstrap",
    "brown",
    "coef",
    "hansen",
    "logLik",
    "ouchtree",
    "paint",
    "plot",
    "print",
    "show",
    "simulate",
    "summary",
    "update"
  ],
  "_datasets": [
    {
      "name": "anolis.ssd",
      "title": "Greater Antillean anolis lizard sexual size dimorphism data",
      "object": "anolis.ssd",
      "class": [
        "data.frame"
      ],
      "fields": [
        "node",
        "species",
        "log.SSD",
        "ancestor",
        "time",
        "OU.1",
        "OU.7"
      ],
      "rows": 38,
      "table": true,
      "tojson": true
    },
    {
      "name": "bimac",
      "title": "Anolis bimaculatus lizard size data",
      "object": "bimac",
      "class": [
        "data.frame"
      ],
      "fields": [
        "node",
        "spcode",
        "species",
        "island",
        "size",
        "ancestor",
        "time",
        "OU.1",
        "OU.3",
        "OU.4",
        "OU.LP"
      ],
      "rows": 45,
      "table": true,
      "tojson": true
    },
    {
      "name": "geospiza",
      "title": "Data on Darwin's finches",
      "object": "geospiza",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "package",
      "title": "Ornstein-Uhlenbeck methods for comparative phylogenetic hypotheses",
      "concept": [
        "examples",
        "methods for ouch trees",
        "phylogenetic comparative models"
      ],
      "topics": [
        "ouch-package",
        "ouch",
        "ouch,package"
      ]
    },
    {
      "page": "anolis_ssd",
      "title": "Greater Antillean anolis lizard sexual size dimorphism data",
      "concept": [
        "examples"
      ],
      "topics": [
        "anolis.ssd"
      ]
    },
    {
      "page": "as_data_frame",
      "title": "Coerce an 'ouch' object to a data frame",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "as.data.frame.browntree",
        "as.data.frame.hansentree",
        "as.data.frame.ouchtree",
        "as_data_frame"
      ]
    },
    {
      "page": "bimac",
      "title": "Anolis bimaculatus lizard size data",
      "concept": [
        "examples"
      ],
      "topics": [
        "bimac"
      ]
    },
    {
      "page": "bootstrap",
      "title": "Bootstrapping for uncertainty quantification",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "bootstrap",
        "bootstrap,ANY-method",
        "bootstrap,browntree-method",
        "bootstrap,hansentree-method",
        "bootstrap,missing-method"
      ]
    },
    {
      "page": "brown",
      "title": "Phylogenetic Brownian motion models",
      "concept": [
        "phylogenetic comparative models"
      ],
      "topics": [
        "brown",
        "browntree-class"
      ]
    },
    {
      "page": "coef",
      "title": "Model coefficients",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "coef",
        "coef,browntree-method",
        "coef,hansentree-method"
      ]
    },
    {
      "page": "geospiza",
      "title": "Data on Darwin's finches",
      "concept": [
        "examples"
      ],
      "topics": [
        "geospiza"
      ]
    },
    {
      "page": "hansen",
      "title": "Ornstein-Uhlenbeck models of trait evolution",
      "concept": [
        "phylogenetic comparative models"
      ],
      "topics": [
        "hansen",
        "hansentree-class"
      ]
    },
    {
      "page": "logLik",
      "title": "Log likelihood of a fitted model",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "logLik",
        "logLik,browntree-method",
        "logLik,hansentree-method"
      ]
    },
    {
      "page": "ouchtree",
      "title": "Phylogenetic tree object in 'ouch' format",
      "concept": [
        "phylogenetic comparative models"
      ],
      "topics": [
        "ape2ouch",
        "ouchtree",
        "ouchtree-class"
      ]
    },
    {
      "page": "paint",
      "title": "Painting regimes on a phylogenetic tree",
      "concept": [
        "methods for ouch trees",
        "phylogenetic comparative models"
      ],
      "topics": [
        "paint"
      ]
    },
    {
      "page": "plot",
      "title": "'ouch' plotting functions",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "plot",
        "plot,hansentree-method",
        "plot,ouchtree-method"
      ]
    },
    {
      "page": "simulate",
      "title": "Simulations of a phylogenetic trait model",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "simulate",
        "simulate,browntree-method",
        "simulate,hansentree-method"
      ]
    },
    {
      "page": "summary",
      "title": "Summary methods",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "summary",
        "summary,browntree-method",
        "summary,hansentree-method"
      ]
    },
    {
      "page": "update",
      "title": "Update and refit an 'ouch' model",
      "concept": [
        "methods for ouch trees"
      ],
      "topics": [
        "update",
        "update,browntree-method",
        "update,hansentree-method"
      ]
    }
  ],
  "_readme": "https://github.com/kingaa/ouch/raw/HEAD/README.md",
  "_rundeps": [
    "subplex"
  ],
  "_score": 6.128399268717807,
  "_indexed": false,
  "_nocasepkg": "ouch",
  "_universes": [
    "phylotastic"
  ],
  "_indexurl": "https://kingaa.r-universe.dev/ouch",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.20-0",
      "date": "2026-06-23T23:50:37.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "120820e4246eb6b8471ac9419bf59f0180c1624340c9d8403ea29703c3f68456",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.20-0",
      "date": "2026-06-23T23:49:38.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "34179c1eb5b87c80f7ee2906baa32c328487d7e59c0d62524441ed6d06e0087a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.20-0",
      "date": "2026-06-23T23:51:13.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "6b008ec93852149854d47c6ed2fba78fbc45bdafa903b09e750c42e3ae71ed85",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.20-0",
      "date": "2026-06-23T23:49:57.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "2745532a8f02aeaaa4fdb48c536893ed175278e7c424530fb55c867ade73d8a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.20-0",
      "date": "2026-06-24T00:05:03.000Z",
      "arch": "aarch64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "ddf3d097d23ea8c651c3663d1b5a0bbf7df524c02193ca47f282d768c19c4546",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.20-0",
      "date": "2026-06-24T00:05:30.000Z",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "54b319493b9789e289701b8d73b9f9b39291d4ef00cf0ab9ab9bf1fb5d012cd3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.20-0",
      "date": "2026-06-24T00:05:17.000Z",
      "arch": "aarch64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "4ea15bc9c252024a982a49856943a1c93d084f9f0511a5b30965cf8cf4841e03",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.20-0",
      "date": "2026-06-24T00:07:39.000Z",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "014fd785d543d7383f196f7e8c12b0d115052adc2814af9d8f152d2f81198c2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.20-0",
      "date": "2026-06-23T23:50:25.000Z",
      "arch": "emscripten",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "44bf68f2805a2e3d636cab18b2483ec54d6dc6b19c819c955676601e4446a25b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.20-0",
      "date": "2026-06-23T23:48:47.000Z",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "d68573d546c1e5d193b219d487ab4df276638cd3d366e8c01413c48175259200",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.20-0",
      "date": "2026-06-23T23:48:59.000Z",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "8cee695b028fa634dbcea19980a6cb636689064dae1a215992183e4615deb1ad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.20-0",
      "date": "2026-06-23T23:48:48.000Z",
      "arch": "x86_64",
      "commit": "a81e0bd40ae22798c481fc640a0ffa17ddefa045",
      "fileid": "b61808a81dae4a8227ea31c0bbbf3fed576638e9b8d20181e79f3a3d6b678816",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28064812870"
    }
  ]
}